[Chimera-users] Question about Model Loops Option in Chimera

[Ecem Güngör]

Dear Elanie,

Thanks for your answer.

Even if I set the option you mentioned to 0, it still moves some positions
of the atoms. That's why I could not comprehend the reason.

Ece


Elaine Meng <meng at cgl.ucsf.edu>, 12 Ara 2022 Pzt, 17:39 tarihinde şunu
yazdı:

> Hi Ece,
> There is an option "Allow this many residues adjacent to missing regions
> to move" which you can change to zero instead of the default of one.  Then
> it should not change any atom positions.
>
> See the documentation:
> <
> https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html#building
> >
>
> I don't know the details of the "standard" option, maybe others can
> elaborate. As mentioned in the documentation, if you choose the DOPE option
> instead, it may produce higher-quality results, but it takes longer and is
> also more prone to calculation failure.
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Dec 12, 2022, at 5:38 AM, Ecem Güngör via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
> >
> > Hello,
> >
> > I have a protein crystal structure where some regions are not resolved
> in the crystal. Therefore, I want to predict and fill these regions,
> without touching the rest, by using the Model Loops/Refine Structure option
> of Modeller in Chimera. When I select the non-terminal missing structure as
> a model and standard as a loop modeling protocol, some atoms in the rest of
> the structure are shifted from the original positions. However, I want to
> keep them as they are. Here I would like to ask what standard loop modeling
> protocol corresponds to. Does it also refine or optimize the structure as a
> whole? What does it actually correspond to?
> >
> > Any help would be appreciated. Thanks.
> >
> > Ece
>
>
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